Variant report

Variant	rs10805346
Chromosome Location	chr4:9920347-9920348
allele	C/T
Outlinks	Ensembl UCSC

Chromatin state
Related regulatory elements
Target genes
Other information

No.	Transcrition factor	Chromosome Location	Cell Line	Cell type	Cell Stage	Matched TF binding sites
1	CTCF	chr4:9920242-9920367	GM12878	blood:	n/a	n/a
2	CTCF	chr4:9920244-9920377	GM12892	blood:	n/a	n/a
3	RAD21	chr4:9920214-9920407	GM12878	blood:	n/a	n/a
4	CTCF	chr4:9920276-9920358	GM19238	blood:	n/a	n/a
5	CTCF	chr4:9920260-9920410	GM12865	blood:	n/a	n/a
6	RAD21	chr4:9920164-9920397	GM12878	blood:	n/a	n/a
7	SMC3	chr4:9920183-9920383	GM12878	blood:	n/a	n/a
8	CTCF	chr4:9920178-9920933	GM12878	blood:	n/a	n/a
9	CTCF	chr4:9920266-9920359	H1-hESC	embryonic stem cell:	n/a	n/a
10	CTCF	chr4:9920273-9920350	GM19240	blood:	n/a	n/a
11	CTCF	chr4:9920267-9920974	K562	blood:	n/a	n/a

No.	Distal block	Cell Line	Cell type	Cell Stage
1	chr4:9918331..9921142-chr4:10116868..10118418,2	MCF-7	breast:

Variant related genes	Relation type
ENSG00000249219	TF binding region
ENSG00000223086	Chromatin interaction
ENSG00000071127	Chromatin interaction

Extended variants
information (count: 49 )
Associated
traits (count: 1 )

rSNPs within LD-proxies of this variant (count:19)

rs_ID	r²[population]
rs12649245	0.94[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs13129697	1.00[LWK][hapmap];0.87[MKK][hapmap];0.93[YRI][hapmap];0.88[AFR][1000 genomes]
rs16890905	0.89[CHB][hapmap];0.84[JPT][hapmap];0.96[ASN][1000 genomes]
rs34450770	0.97[ASN][1000 genomes]
rs34752819	0.97[ASN][1000 genomes]
rs3733591	0.89[CHB][hapmap];0.88[JPT][hapmap];0.97[ASN][1000 genomes]
rs4447862	0.82[AFR][1000 genomes]
rs4697695	0.84[GIH][hapmap]
rs6449137	0.82[AFR][1000 genomes]
rs6811809	0.97[ASN][1000 genomes]
rs6823877	0.82[GIH][hapmap]
rs734553	0.84[LWK][hapmap];0.83[YRI][hapmap];0.80[AFR][1000 genomes]
rs737267	0.80[LWK][hapmap]
rs7670751	0.80[LWK][hapmap]
rs7674711	0.94[CHB][hapmap];0.84[JPT][hapmap];0.95[ASN][1000 genomes]
rs7674723	0.95[ASN][1000 genomes]
rs7675964	0.96[LWK][hapmap];0.90[YRI][hapmap]
rs938558	0.93[YRI][hapmap];0.81[AFR][1000 genomes]
rs938564	0.86[YRI][hapmap]

Variant overlapped rSNPs/rCNVs (count:30 , 50 per page) page: 1

No.	Variant name	Chromosome position	Chromatin state	Related regulatory elements	Target genes	Extended variants	Associated traits
1	nsv533218	chr4:9371016-10252290	Active TSS Weak transcription Enhancers Genic enhancers Strong transcription Flanking Active TSS Bivalent Enhancer Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	74 gene(s)	inside rSNPs	diseases
2	nsv530090	chr4:9383695-10165033	Enhancers Genic enhancers Flanking Active TSS Weak transcription Flanking Bivalent TSS/Enh Strong transcription Bivalent Enhancer Bivalent/Poised TSS Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	70 gene(s)	inside rSNPs	diseases
3	nsv1014216	chr4:9713612-10223836	Transcr. at gene 5' and 3' Genic enhancers Enhancers Strong transcription Flanking Active TSS Bivalent/Poised TSS Weak transcription Bivalent Enhancer Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	53 gene(s)	inside rSNPs	diseases
4	nsv1010249	chr4:9716101-10086188	Strong transcription Enhancers Weak transcription Bivalent Enhancer Flanking Active TSS Active TSS Genic enhancers ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	15 gene(s)	inside rSNPs	diseases
5	nsv878672	chr4:9786732-10008305	Flanking Active TSS Enhancers Weak transcription Active TSS ZNF genes & repeats Strong transcription Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
6	nsv878676	chr4:9797703-9978094	Weak transcription Strong transcription Genic enhancers Enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Bivalent TSS/Enh Flanking Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
7	nsv878677	chr4:9797703-10008305	Enhancers Genic enhancers Flanking Active TSS Weak transcription Strong transcription Bivalent Enhancer ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
8	nsv1007593	chr4:9802146-9956285	Strong transcription Weak transcription Enhancers Genic enhancers ZNF genes & repeats Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
9	nsv878681	chr4:9802853-10397327	Enhancers Weak transcription ZNF genes & repeats Strong transcription Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Active TSS Flanking Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
10	nsv997941	chr4:9805223-10493388	Weak transcription Enhancers Strong transcription Flanking Active TSS Genic enhancers Active TSS Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent Enhancer Flanking Bivalent TSS/Enh Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	54 gene(s)	inside rSNPs	diseases
11	nsv1008649	chr4:9805223-10589802	Weak transcription Enhancers Genic enhancers Flanking Active TSS ZNF genes & repeats Strong transcription Bivalent Enhancer Transcr. at gene 5' and 3' Active TSS Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
12	nsv1000587	chr4:9805223-10610752	Flanking Active TSS Enhancers Genic enhancers Weak transcription ZNF genes & repeats Active TSS Flanking Bivalent TSS/Enh Bivalent/Poised TSS Transcr. at gene 5' and 3' Strong transcription Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
13	nsv537022	chr4:9805223-10610752	Enhancers Strong transcription Flanking Active TSS ZNF genes & repeats Weak transcription Active TSS Genic enhancers Transcr. at gene 5' and 3' Bivalent Enhancer Bivalent/Poised TSS Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	56 gene(s)	inside rSNPs	diseases
14	nsv1003454	chr4:9805223-10710990	Enhancers Weak transcription Flanking Active TSS Strong transcription Genic enhancers Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent/Poised TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
15	nsv537023	chr4:9805223-10710990	Weak transcription Enhancers Strong transcription Flanking Active TSS Transcr. at gene 5' and 3' Genic enhancers Bivalent/Poised TSS Flanking Bivalent TSS/Enh Active TSS ZNF genes & repeats Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
16	nsv1004801	chr4:9814720-10674528	Enhancers Strong transcription Flanking Bivalent TSS/Enh Weak transcription Active TSS Flanking Active TSS Genic enhancers Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS Bivalent Enhancer	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
17	nsv537024	chr4:9814720-10674528	Weak transcription Genic enhancers Enhancers Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3' ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	57 gene(s)	inside rSNPs	diseases
18	nsv931483	chr4:9814721-10716463	Strong transcription Bivalent/Poised TSS Flanking Active TSS Genic enhancers Enhancers Weak transcription Active TSS Flanking Bivalent TSS/Enh Bivalent Enhancer Transcr. at gene 5' and 3' ZNF genes & repeats	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
19	nsv1004311	chr4:9825814-9978414	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
20	nsv998425	chr4:9834666-9961280	Enhancers Weak transcription Genic enhancers Strong transcription Active TSS ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
21	esv2763339	chr4:9858426-10056376	Enhancers Flanking Active TSS Active TSS Weak transcription Strong transcription Genic enhancers Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	6 gene(s)	inside rSNPs	diseases
22	nsv878684	chr4:9863698-9998440	Enhancers Weak transcription Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Genic enhancers Flanking Active TSS Active TSS Bivalent Enhancer Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
23	nsv878686	chr4:9893403-10008305	Flanking Active TSS Weak transcription Strong transcription Enhancers ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Bivalent TSS/Enh Active TSS Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
24	nsv537026	chr4:9903566-10262258	Enhancers Weak transcription Flanking Bivalent TSS/Enh Genic enhancers Transcr. at gene 5' and 3' Flanking Active TSS Strong transcription Active TSS Bivalent Enhancer ZNF genes & repeats Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	48 gene(s)	inside rSNPs	diseases
25	nsv1009972	chr4:9903566-10710990	Genic enhancers Enhancers Strong transcription Active TSS Flanking Active TSS Transcr. at gene 5' and 3' Weak transcription Bivalent Enhancer Bivalent/Poised TSS ZNF genes & repeats Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
26	nsv537027	chr4:9903566-10710990	Flanking Active TSS ZNF genes & repeats Active TSS Weak transcription Enhancers Strong transcription Genic enhancers Bivalent/Poised TSS Transcr. at gene 5' and 3' Bivalent Enhancer Flanking Bivalent TSS/Enh	TF binding region CpG island Chromatin interactive region lncRNA miRNA	58 gene(s)	inside rSNPs	diseases
27	esv2752052	chr4:9911872-10313111	Genic enhancers Weak transcription Enhancers Flanking Active TSS Strong transcription Transcr. at gene 5' and 3' Active TSS ZNF genes & repeats Flanking Bivalent TSS/Enh Bivalent Enhancer Bivalent/Poised TSS	TF binding region CpG island Chromatin interactive region lncRNA miRNA	51 gene(s)	inside rSNPs	diseases
28	nsv527211	chr4:9912101-9944650	Weak transcription Enhancers Genic enhancers Strong transcription Flanking Bivalent TSS/Enh ZNF genes & repeats Flanking Active TSS Bivalent Enhancer Active TSS	TF binding region CpG island Chromatin interactive region lncRNA	4 gene(s)	inside rSNPs	diseases
29	nsv878687	chr4:9912101-10008305	Weak transcription Enhancers Strong transcription ZNF genes & repeats Genic enhancers Bivalent Enhancer Flanking Active TSS Active TSS Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases
30	nsv878688	chr4:9915850-10038112	Weak transcription Bivalent Enhancer Enhancers Flanking Active TSS Active TSS Strong transcription Bivalent/Poised TSS Genic enhancers ZNF genes & repeats Flanking Bivalent TSS/Enh Transcr. at gene 5' and 3'	TF binding region CpG island Chromatin interactive region lncRNA	5 gene(s)	inside rSNPs	diseases

mRNA abundance (count:1)

SNP	Gene	Cis/trans	Tissue	Source
rs10805346	CRMP1	cis	parietal	SCAN

Chromatin state (count:30 , 50 per page) page: 1

No.	Chromosome Location	Chromatin state	Cell line	Tissue
1	chr4:9897000-9924600	Strong transcription	Breast Myoepithelial Primary Cells	Breast
2	chr4:9903400-9923200	Strong transcription	HepG2	liver
3	chr4:9903600-9928600	Strong transcription	Primary monocytes fromperipheralblood	blood
4	chr4:9903600-9929000	Strong transcription	Monocytes-CD14+_RO01746	blood
5	chr4:9907400-9923200	Strong transcription	Foreskin Keratinocyte Primary Cells skin02	Skin
6	chr4:9908000-9943000	Weak transcription	Primary mononuclear cells fromperipheralblood	Blood
7	chr4:9911400-9979800	Weak transcription	Duodenum Smooth Muscle	Duodenum
8	chr4:9914200-9926000	Weak transcription	Spleen	Spleen
9	chr4:9914400-9922800	Strong transcription	HMEC	breast
10	chr4:9915400-9928000	Strong transcription	Fetal Intestine Small	intestine
11	chr4:9916000-9921200	Strong transcription	Liver	Liver
12	chr4:9917000-9922600	Weak transcription	ES-I3 Cell Line	embryonic stem cell
13	chr4:9917400-9923400	Strong transcription	Foreskin Keratinocyte Primary Cells skin03	Skin
14	chr4:9918000-9920400	Enhancers	Right Atrium	heart
15	chr4:9918600-9948600	Weak transcription	Pancreas	Pancrea
16	chr4:9918800-9920600	Weak transcription	Skeletal Muscle Male	skeletal muscle
17	chr4:9918800-9921200	Weak transcription	Left Ventricle	heart
18	chr4:9919000-9922400	Weak transcription	H1 BMP4 Derived Mesendoderm Cultured Cells	ES cell derived
19	chr4:9919200-9922800	Strong transcription	NHEK	skin
20	chr4:9919400-9920400	Strong transcription	Duodenum Mucosa	Duodenum
21	chr4:9919400-9920400	Enhancers	Right Ventricle	heart
22	chr4:9919400-9921200	Strong transcription	Esophagus	oesophagus
23	chr4:9919400-9922600	Weak transcription	iPS DF 19.11 Cell Line	embryonic stem cell
24	chr4:9919600-9922800	Strong transcription	Fetal Intestine Large	intestine
25	chr4:9919600-9923600	Strong transcription	Breast variant Human Mammary Epithelial Cells (vHMEC)	Breast
26	chr4:9919800-9920400	Genic enhancers	Fetal Muscle Trunk	muscle
27	chr4:9920000-9921400	Strong transcription	Lung	lung
28	chr4:9920200-9921600	Enhancers	Skeletal Muscle Female	skeletal muscle
29	chr4:9920200-9921600	Strong transcription	Stomach Smooth Muscle	stomach
30	chr4:9920200-9943400	Weak transcription	Aorta	Aorta

The 2.0 version of rSNPBase

Variant report

Quick Search:

what's new

Quick links